TB-Profiler result

Run: SRR29539559
Summary

Run ID: SRR29539559

Sample name:

Date: 2024-10-04T03:16:26.314471

Number of reads: 3034856

Percentage reads mapped: 99.64

Median coverage: 78.0

Strain: lineage4.1.2;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.42
lineage4.1 Euro-American None 0.59
lineage4.1.2 Euro-American None 0.57
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.37
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
rpoC p.Gly332Arg Uncertain significance Mutation from literature
isoniazid inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761155 p.Ser450Leu missense_variant 0.49 rifampicin Assoc w R
rpoC 764363 p.Gly332Arg missense_variant 0.35 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.32 streptomycin Assoc w R
inhA 1673423 c.-779G>T upstream_gene_variant 0.52 ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.39 isoniazid Assoc w R High-level resistance
eis 2715342 c.-10G>A upstream_gene_variant 0.48 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
embB 4247431 p.Met306Ile missense_variant 0.46 ethambutol Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.26 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.6 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.66 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.59 rifampicin Not assoc w R
rpoC 764263 c.894G>A synonymous_variant 0.53 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.37 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.62 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777320 c.1161C>G synonymous_variant 0.58 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800200 c.-609C>G upstream_gene_variant 0.56 linezolid
Rv1129c 1253304 p.Asn411Tyr missense_variant 0.43 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471644 n.-202T>C upstream_gene_variant 0.58 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.44 pyrazinamide Not assoc w R - Interim
tsnR 1853513 c.-93C>A upstream_gene_variant 0.33 linezolid
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918584 c.645A>C synonymous_variant 0.67 capreomycin Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.57 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.31 isoniazid
Rv2477c 2783478 p.His189Tyr missense_variant 0.48 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2477c 2783740 p.Asp101Glu missense_variant 0.7 kanamycin
levofloxacin
moxifloxacin
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin
ribD 2986827 c.-12G>A upstream_gene_variant 0.49 para-aminosalicylic_acid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.23 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.17 capreomycin
Rv2752c 3067135 c.-944C>T upstream_gene_variant 0.43 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.4 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3611974 c.1143A>C synonymous_variant 0.59 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
ddn 3987104 p.Met87Ile missense_variant 0.45 pretomanid
delamanid Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.45 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.65 ethambutol Not assoc w R
embA 4243217 c.-16C>A upstream_gene_variant 0.42 ethambutol Uncertain significance
embB 4248365 p.Val618Met missense_variant 0.58 ethambutol Uncertain significance
ubiA 4269615 c.219C>T synonymous_variant 0.34 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407720 c.483C>G synonymous_variant 0.28 streptomycin Not assoc w R - Interim
gid 4408156 p.Leu16Arg missense_variant 0.38 streptomycin Not assoc w R